diff --git a/internal/bzlmod/default_gazelle_overrides.bzl b/internal/bzlmod/default_gazelle_overrides.bzl
index 3492a4f..aa6c120 100644
--- a/internal/bzlmod/default_gazelle_overrides.bzl
+++ b/internal/bzlmod/default_gazelle_overrides.bzl
@@ -15,6 +15,7 @@
 visibility("private")
 
 DEFAULT_BUILD_FILE_GENERATION_BY_PATH = {
+    "github.com/bazelbuild/bazelisk": "on",
     "github.com/envoyproxy/protoc-gen-validate": "on",
     "github.com/google/safetext": "on",
     "github.com/grpc-ecosystem/grpc-gateway/v2": "on",
diff --git a/language/go/config.go b/language/go/config.go
index d0a4007..72c31da 100644
--- a/language/go/config.go
+++ b/language/go/config.go
@@ -492,6 +492,10 @@
 		gc.submodules = append(gc.submodules, m)
 	}
 
+	// This is a hack to inject into the ApparentLoads function, which does not
+	// receive the configuration - other languages shouldn't need to do this.
+	isGoRepositoryMode = gc.goRepositoryMode
+
 	return nil
 }
 
diff --git a/language/go/kinds.go b/language/go/kinds.go
index 0f465f0..907b4e9 100644
--- a/language/go/kinds.go
+++ b/language/go/kinds.go
@@ -17,6 +17,8 @@
 
 import (
 	"fmt"
+	"log"
+
 	"github.com/bazelbuild/bazel-gazelle/rule"
 )
 
@@ -174,7 +176,15 @@
 	return apparentLoads(moduleToApparentName)
 }
 
+var isGoRepositoryMode = false
+
 func apparentLoads(moduleToApparentName func(string) string) []rule.LoadInfo {
+	if isGoRepositoryMode {
+		// Repositories generated by a module extension, such as go_deps, have
+		// to use the apparent name used by the module that contains the
+		// extension, which in the case of gazelle are the legacy names.
+		moduleToApparentName = func(s string) string { return "" }
+	}
 	rulesGo := moduleToApparentName("rules_go")
 	if rulesGo == "" {
 		rulesGo = "io_bazel_rules_go"
@@ -183,6 +193,7 @@
 	if gazelle == "" {
 		gazelle = "bazel_gazelle"
 	}
+	log.Println("rulesGo: ", rulesGo)
 
 	return []rule.LoadInfo{
 		{
diff --git a/merger/fix.go b/merger/fix.go
index 38759fb..3a1d8ce 100644
--- a/merger/fix.go
+++ b/merger/fix.go
@@ -42,9 +42,9 @@
 	// statements and not deleted statements.
 	f.Sync()
 
-	// Scan load statements in the file. Keep track of loads of known files,
-	// since these may be changed. Keep track of symbols loaded from unknown
-	// files; we will not add loads for these.
+	// Scan load statements in the file. Keep track of loads of known files
+	// and symbols since these may be changed. Keep track of symbols loaded
+	// from unknown files; we will not add loads for these.
 	var loads []*rule.Load
 	otherLoadedKinds := make(map[string]bool)
 	for _, l := range f.Loads {
@@ -52,8 +52,16 @@
 			loads = append(loads, l)
 			continue
 		}
+		seenKnownSymbol := false
 		for _, sym := range l.Symbols() {
-			otherLoadedKinds[sym] = true
+			if _, ok := knownSymbols[sym]; ok {
+				if !seenKnownSymbol {
+					loads = append(loads, l)
+					seenKnownSymbol = true
+				}
+			} else {
+				otherLoadedKinds[sym] = true
+			}
 		}
 	}
 
@@ -146,6 +154,8 @@
 			return nil
 		}
 		load = rule.NewLoad(file)
+	} else if load.Name() != file {
+		load.SetName(file)
 	}
 
 	for k := range symbols {
diff --git a/merger/fix_test.go b/merger/fix_test.go
index 53f4dcc..7f935c6 100644
--- a/merger/fix_test.go
+++ b/merger/fix_test.go
@@ -237,6 +237,16 @@
 )
 `,
 		},
+		"incorrect load": {
+			input: `load("@not_foo", "foo_binary")
+
+foo_binary(name = "a")
+`,
+			want: `load("@foo", "foo_binary")
+
+foo_binary(name = "a")
+`,
+		},
 	} {
 		t.Run(name, func(t *testing.T) {
 			f, err := rule.LoadData("", "", []byte(tc.input))
diff --git a/rule/rule.go b/rule/rule.go
index b15f87f..1385fa1 100644
--- a/rule/rule.go
+++ b/rule/rule.go
@@ -604,6 +604,11 @@
 	return l.name
 }
 
+func (l *Load) SetName(name string) {
+	l.name = name
+	l.updated = true
+}
+
 // Symbols returns a sorted list of symbols this statement loads.
 // If the symbol is loaded with a name different from its definition, the
 // loaded name is returned, not the original name.
diff --git a/tests/bcr/go_mod/MODULE.bazel b/tests/bcr/go_mod/MODULE.bazel
index 0317b60..34b8807 100644
--- a/tests/bcr/go_mod/MODULE.bazel
+++ b/tests/bcr/go_mod/MODULE.bazel
@@ -136,6 +136,7 @@
 )
 use_repo(
     go_deps,
+    "com_github_bazelbuild_bazelisk",
     "com_github_bazelbuild_buildtools",
     "com_github_bmatcuk_doublestar_v4",
     "com_github_datadog_sketches_go",
diff --git a/tests/bcr/go_mod/go.mod b/tests/bcr/go_mod/go.mod
index 0b6325c..f1dff65 100644
--- a/tests/bcr/go_mod/go.mod
+++ b/tests/bcr/go_mod/go.mod
@@ -9,6 +9,8 @@
 require (
 	example.org/hello v1.0.0
 	github.com/DataDog/sketches-go v1.4.1
+	// NOTE: Keep at v1.25.0 to test rewriting of load statements
+	github.com/bazelbuild/bazelisk v1.25.0
 	github.com/bazelbuild/buildtools v0.0.0-20230317132445-9c3c1fc0106e
 	github.com/bazelbuild/rules_go v0.39.1
 	// NOTE: keep <4.7.0 to test the 'replace'
@@ -18,17 +20,22 @@
 	github.com/fmeum/dep_on_gazelle v1.0.0
 	github.com/google/go-jsonnet v0.20.0
 	github.com/google/safetext v0.0.0-20220905092116-b49f7bc46da2
-	github.com/stretchr/testify v1.6.1
-	golang.org/x/sys v0.15.0
+	github.com/stretchr/testify v1.9.0
+	golang.org/x/sys v0.27.0
 )
 
+require google.golang.org/protobuf v1.32.0
+
 require (
 	github.com/bazelbuild/bazel-gazelle v0.30.0 // indirect
-	github.com/davecgh/go-spew v1.1.0 // indirect
-	github.com/kr/text v0.2.0 // indirect
+	github.com/bgentry/go-netrc v0.0.0-20140422174119-9fd32a8b3d3d // indirect
+	github.com/davecgh/go-spew v1.1.1 // indirect
+	github.com/kr/pretty v0.3.1 // indirect
+	github.com/mitchellh/go-homedir v1.1.0 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
+	golang.org/x/term v0.26.0 // indirect
 	golang.org/x/text v0.9.0 // indirect
-	google.golang.org/protobuf v1.32.0 // indirect
+	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c // indirect
 	gopkg.in/yaml.v2 v2.2.7 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect
 	rsc.io/quote v1.5.2 // indirect
diff --git a/tests/bcr/go_mod/go.sum b/tests/bcr/go_mod/go.sum
index bdbc4f8..e91a91e 100644
--- a/tests/bcr/go_mod/go.sum
+++ b/tests/bcr/go_mod/go.sum
@@ -4,12 +4,16 @@
 github.com/DataDog/sketches-go v1.4.1/go.mod h1:xJIXldczJyyjnbDop7ZZcLxJdV3+7Kra7H1KMgpgkLk=
 github.com/bazelbuild/bazel-gazelle v0.30.0 h1:q9XLWQSCA5NZPJ98WFqicHkq6fxrDPnfvMO1XycQBMg=
 github.com/bazelbuild/bazel-gazelle v0.30.0/go.mod h1:6RxhjM1v/lTpD3JlMpKUCcdus4tvdqsqdfbjYi+czYs=
+github.com/bazelbuild/bazelisk v1.25.0 h1:sMoyCM+x6tsc8CI0INJW1+izZgn3RlY8P++hg0Hdbek=
+github.com/bazelbuild/bazelisk v1.25.0/go.mod h1:EcD+apTi37Jq7m9B2eXXCO/xxd8FoSeUwmNsIxb7uDo=
 github.com/bazelbuild/buildtools v0.0.0-20230317132445-9c3c1fc0106e h1:XmPu4mXICgdGnC5dXGjUGbwUD/kUmS0l5Aop3LaevBM=
 github.com/bazelbuild/buildtools v0.0.0-20230317132445-9c3c1fc0106e/go.mod h1:689QdV3hBP7Vo9dJMmzhoYIyo/9iMhEmHkJcnaPRCbo=
 github.com/bazelbuild/rules_go v0.39.1 h1:wkJLUDx59dntWMghuL8++GteoU1To6sRoKJXuyFtmf8=
 github.com/bazelbuild/rules_go v0.39.1/go.mod h1:TMHmtfpvyfsxaqfL9WnahCsXMWDMICTw7XeK9yVb+YU=
-github.com/bmatcuk/doublestar v1.3.4 h1:gPypJ5xD31uhX6Tf54sDPUOBXTqKH4c9aPY66CyQrS0=
-github.com/bmatcuk/doublestar v1.3.4/go.mod h1:wiQtGV+rzVYxB7WIlirSN++5HPtPlXEo9MEoZQC/PmE=
+github.com/bgentry/go-netrc v0.0.0-20140422174119-9fd32a8b3d3d h1:xDfNPAt8lFiC1UJrqV3uuy861HCTo708pDMbjHHdCas=
+github.com/bgentry/go-netrc v0.0.0-20140422174119-9fd32a8b3d3d/go.mod h1:6QX/PXZ00z/TKoufEY6K/a0k6AhaJrQKdFe6OfVXsa4=
+github.com/bmatcuk/doublestar/v4 v4.7.1 h1:fdDeAqgT47acgwd9bd9HxJRDmc9UAmPpc+2m0CXv75Q=
+github.com/bmatcuk/doublestar/v4 v4.7.1/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
 github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU=
 github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI=
 github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI=
@@ -18,8 +22,9 @@
 github.com/cloudflare/circl v1.3.7 h1:qlCDlTPz2n9fu58M0Nh1J/JzcFpfgkFHHX3O35r5vcU=
 github.com/cloudflare/circl v1.3.7/go.mod h1:sRTcRWXGLrKw6yIGJ+l7amYJFfAXbZG0kBSc8r4zxgA=
 github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
-github.com/davecgh/go-spew v1.1.0 h1:ZDRjVQ15GmhC3fiQ8ni8+OwkZQO4DARzQgrnXU1Liz8=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
+github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/envoyproxy/go-control-plane v0.9.1-0.20191026205805-5f8ba28d4473/go.mod h1:YTl/9mNaCwkRvm6d1a2C3ymFceY/DCBVvsKhRF0iEA4=
 github.com/envoyproxy/protoc-gen-validate v0.1.0/go.mod h1:iSmxcyjqTsJpI2R4NaDN7+kN2VEUnK/pcBlmesArF7c=
 github.com/envoyproxy/protoc-gen-validate v1.0.1 h1:kt9FtLiooDc0vbwTLhdg3dyNX1K9Qwa1EK9LcD4jVUQ=
@@ -55,16 +60,27 @@
 github.com/google/gofuzz v1.2.0/go.mod h1:dBl0BpW6vV/+mYPU4Po3pmUjxk6FQPldtuIdl/M65Eg=
 github.com/google/safetext v0.0.0-20220905092116-b49f7bc46da2 h1:SJ+NtwL6QaZ21U+IrK7d0gGgpjGGvd2kz+FzTHVzdqI=
 github.com/google/safetext v0.0.0-20220905092116-b49f7bc46da2/go.mod h1:Tv1PlzqC9t8wNnpPdctvtSUOPUUg4SHeE6vR1Ir2hmg=
+github.com/kr/pretty v0.2.1/go.mod h1:ipq/a2n7PKx3OHsz4KJII5eveXtPO4qwEXGdVfWzfnI=
+github.com/kr/pretty v0.3.1 h1:flRD4NNwYAUpkphVc1HcthR4KEIFJ65n8Mw5qdRn3LE=
+github.com/kr/pretty v0.3.1/go.mod h1:hoEshYVHaxMs3cyo3Yncou5ZscifuDolrwPKZanG3xk=
+github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
+github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
 github.com/kr/text v0.2.0 h1:5Nx0Ya0ZqY2ygV366QzturHI13Jq95ApcVaJBhpS+AY=
 github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE=
-github.com/niemeyer/pretty v0.0.0-20200227124842-a10e7caefd8e h1:fD57ERR4JtEqsWbfPhv4DMiApHyliiK5xCTNVSPiaAs=
-github.com/niemeyer/pretty v0.0.0-20200227124842-a10e7caefd8e/go.mod h1:zD1mROLANZcx1PVRCS0qkT7pwLkGfwJo4zjcN/Tysno=
+github.com/mitchellh/go-homedir v1.1.0 h1:lukF9ziXFxDFPkA1vsr5zpc1XuPDn/wFntq5mG+4E0Y=
+github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0=
+github.com/pkg/diff v0.0.0-20210226163009-20ebb0f2a09e/go.mod h1:pJLUxLENpZxwdsKMEsNbx1VGcRFpLqf3715MtcvvzbA=
 github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/prometheus/client_model v0.0.0-20190812154241-14fe0d1b01d4/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA=
+github.com/rogpeppe/go-internal v1.9.0 h1:73kH8U+JUqXU8lRuOHeVHaa/SZPifC7BkcraZVejAe8=
+github.com/rogpeppe/go-internal v1.9.0/go.mod h1:WtVeX8xhTBvf0smdhujwtBcq4Qrzq/fJaraNFVN+nFs=
+github.com/sergi/go-diff v1.1.0 h1:we8PVUC3FE2uYfodKH/nBHMSetSfHDR6scGdBi+erh0=
+github.com/sergi/go-diff v1.1.0/go.mod h1:STckp+ISIX8hZLjrqAeVduY0gWCT9IjLuqbuNXdaHfM=
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
-github.com/stretchr/testify v1.6.1 h1:hDPOHmpOpP40lSULcqw7IrRb/u7w6RpDC9399XyoNd0=
 github.com/stretchr/testify v1.6.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
+github.com/stretchr/testify v1.9.0 h1:HtqpIVDClZ4nwg75+f6Lvsy/wHu+3BoSGCbBAcpTsTg=
+github.com/stretchr/testify v1.9.0/go.mod h1:r2ic/lqez/lEtzL7wO/rwa5dbSLXVDPFyf8C91i36aY=
 go.starlark.net v0.0.0-20210223155950-e043a3d3c984/go.mod h1:t3mmBBPzAVvK0L0n1drDmrQsJ8FoIx4INCqVMTr/Zo0=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/exp v0.0.0-20190121172915-509febef88a4/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
@@ -82,8 +98,10 @@
 golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
 golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
 golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/sys v0.15.0 h1:h48lPFYpsTvQJZF4EKyI4aLHaev3CxivZmv7yZig9pc=
-golang.org/x/sys v0.15.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
+golang.org/x/sys v0.27.0 h1:wBqf8DvsY9Y/2P8gAfPDEYNuS30J4lPHJxXSb/nJZ+s=
+golang.org/x/sys v0.27.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
+golang.org/x/term v0.26.0 h1:WEQa6V3Gja/BhNxg540hBip/kkaYtRg3cxg4oXSw4AU=
+golang.org/x/term v0.26.0/go.mod h1:Si5m1o57C5nBNQo5z1iq+XDijt21BDBDp2bK0QI8e3E=
 golang.org/x/text v0.0.0-20170915032832-14c0d48ead0c/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
 golang.org/x/text v0.9.0 h1:2sjJmO8cDvYveuX97RDLsxlyUxLl+GHoLxBiRdHllBE=
@@ -117,8 +135,8 @@
 google.golang.org/protobuf v1.32.0 h1:pPC6BG5ex8PDFnkbrGU3EixyhKcQ2aDuBS36lqK/C7I=
 google.golang.org/protobuf v1.32.0/go.mod h1:c6P6GXX6sHbq/GpV6MGZEdwhWPcYBgnhAHhKbcUYpos=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/check.v1 v1.0.0-20200902074654-038fdea0a05b h1:QRR6H1YWRnHb4Y/HeNFCTJLFVxaq6wH4YuVdsUOr75U=
-gopkg.in/check.v1 v1.0.0-20200902074654-038fdea0a05b/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
+gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
 gopkg.in/yaml.v2 v2.2.7 h1:VUgggvou5XRW9mHwD/yXxIYSMtY0zoKQf/v226p2nyo=
 gopkg.in/yaml.v2 v2.2.7/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
diff --git a/tests/bcr/go_mod/pkg/BUILD.bazel b/tests/bcr/go_mod/pkg/BUILD.bazel
index 66dc22d..e28940d 100644
--- a/tests/bcr/go_mod/pkg/BUILD.bazel
+++ b/tests/bcr/go_mod/pkg/BUILD.bazel
@@ -53,6 +53,7 @@
     deps = [
         "//pkg/data",
         "@circl//dh/x25519",
+        "@com_github_bazelbuild_bazelisk//httputil",
         "@com_github_bazelbuild_buildtools//labels:go_default_library",
         "@com_github_bmatcuk_doublestar_v4//:doublestar",
         "@com_github_datadog_sketches_go//ddsketch",
diff --git a/tests/bcr/go_mod/pkg/pkg_test.go b/tests/bcr/go_mod/pkg/pkg_test.go
index 1956fde..b0d5fe5 100644
--- a/tests/bcr/go_mod/pkg/pkg_test.go
+++ b/tests/bcr/go_mod/pkg/pkg_test.go
@@ -7,6 +7,7 @@
 
 	"example.org/hello"
 	"github.com/DataDog/sketches-go/ddsketch"
+	"github.com/bazelbuild/bazelisk/httputil"
 	"github.com/bazelbuild/bazel-gazelle/tests/bcr/go_mod/pkg/data"
 	"github.com/bazelbuild/buildtools/labels"
 	"github.com/bazelbuild/rules_go/go/runfiles"
@@ -89,3 +90,9 @@
 	// the module path with a file path.
 	require.Equal(t, "Hello, world.", hello.Hello())
 }
+
+func TestDepWithRewrittenLoad(t *testing.T) {
+	// Bazelisk's httputil package refers to rules_go as `@rules_go` in its load statement, not as
+	// `@io_bazel_rules_go`.
+	require.NotEmpty(t, httputil.UserAgent)
+}