diff --git a/.changeset/rude-clocks-prove.md b/.changeset/rude-clocks-prove.md
new file mode 100644
index 00000000000..7496b7fc931
--- /dev/null
+++ b/.changeset/rude-clocks-prove.md
@@ -0,0 +1,6 @@
+---
+"@remix-run/dev": minor
+---
+
+- Log deprecation warnings for v3 future flags
+- Add `@deprecated` annotations to `json`/`defer` utilities
diff --git a/integration/vite-build-test.ts b/integration/vite-build-test.ts
index dd6c7681b63..6918143be14 100644
--- a/integration/vite-build-test.ts
+++ b/integration/vite-build-test.ts
@@ -40,7 +40,15 @@ test.beforeAll(async () => {
         },
         plugins: [
           mdx(),
-          remix(),
+          remix({
+            future: {
+              v3_fetcherPersist: true,
+              v3_lazyRouteDiscovery: true,
+              v3_relativeSplatPath: true,
+              v3_singleFetch: true,
+              v3_throwAbortReason: true,
+            }
+          }),
         ],
       });
     `,
diff --git a/integration/vite-css-test.ts b/integration/vite-css-test.ts
index de37c65ce2c..77bc5ccc2f6 100644
--- a/integration/vite-css-test.ts
+++ b/integration/vite-css-test.ts
@@ -44,7 +44,7 @@ const files = {
   `,
   "app/entry.client.tsx": js`
     import "./entry.client.css";
-  
+
     import { RemixBrowser } from "@remix-run/react";
     import { startTransition, StrictMode } from "react";
     import { hydrateRoot } from "react-dom/client";
@@ -156,7 +156,18 @@ const VITE_CONFIG = async (port: number) => dedent`
 
   export default {
     ${await viteConfig.server({ port })}
-    plugins: [remix(), vanillaExtractPlugin()],
+    plugins: [
+      remix({
+        future: {
+          v3_fetcherPersist: true,
+          v3_lazyRouteDiscovery: true,
+          v3_relativeSplatPath: true,
+          v3_singleFetch: true,
+          v3_throwAbortReason: true,
+        }
+      }),
+      vanillaExtractPlugin()
+    ],
   }
 `;
 
diff --git a/integration/vite-presets-test.ts b/integration/vite-presets-test.ts
index e190f2289d5..1859c028a1c 100644
--- a/integration/vite-presets-test.ts
+++ b/integration/vite-presets-test.ts
@@ -26,6 +26,13 @@ const files = {
         assetsDir: "custom-assets-dir",
       },
       plugins: [remix({
+        future: {
+          v3_fetcherPersist: true,
+          v3_lazyRouteDiscovery: true,
+          v3_relativeSplatPath: true,
+          v3_singleFetch: true,
+          v3_throwAbortReason: true,
+        },
         presets: [
           // Ensure user config is passed to remixConfig hook
           {
@@ -35,7 +42,16 @@ const files = {
                 throw new Error("Remix user config doesn't have presets array.");
               }
 
-              let expected = JSON.stringify({ appDirectory: "app"});
+              let expected = JSON.stringify({
+                future: {
+                  v3_fetcherPersist: true,
+                  v3_lazyRouteDiscovery: true,
+                  v3_relativeSplatPath: true,
+                  v3_singleFetch: true,
+                  v3_throwAbortReason: true,
+                },
+                appDirectory: "app",
+              });
               let actual = JSON.stringify(restUserConfig);
 
               if (actual !== expected) {
@@ -49,7 +65,7 @@ const files = {
               return {};
             },
           },
-          
+
           // Ensure preset config takes lower precedence than user config
           {
             name: "test-preset",
diff --git a/packages/remix-dev/config.ts b/packages/remix-dev/config.ts
index 247a4c3f8cb..0d94a5f2287 100644
--- a/packages/remix-dev/config.ts
+++ b/packages/remix-dev/config.ts
@@ -1,17 +1,17 @@
+import type { NodePolyfillsOptions as EsbuildPluginsNodeModulesPolyfillOptions } from "esbuild-plugins-node-modules-polyfill";
+import fse from "fs-extra";
 import { execSync } from "node:child_process";
 import path from "node:path";
 import { pathToFileURL } from "node:url";
-import fse from "fs-extra";
-import type { NodePolyfillsOptions as EsbuildPluginsNodeModulesPolyfillOptions } from "esbuild-plugins-node-modules-polyfill";
 
-import type { RouteManifest, DefineRoutesFunction } from "./config/routes";
-import { defineRoutes } from "./config/routes";
-import { ServerMode, isValidServerMode } from "./config/serverModes";
-import { serverBuildVirtualModule } from "./compiler/server/virtualModules";
-import { flatRoutes } from "./config/flat-routes";
 import { detectPackageManager } from "./cli/detectPackageManager";
-import { tryLoadPackageJson } from "./cli/tryLoadPackageJson";
 import { detectServerRuntime } from "./cli/detectServerRuntime";
+import { tryLoadPackageJson } from "./cli/tryLoadPackageJson";
+import { serverBuildVirtualModule } from "./compiler/server/virtualModules";
+import { flatRoutes } from "./config/flat-routes";
+import type { DefineRoutesFunction, RouteManifest } from "./config/routes";
+import { defineRoutes } from "./config/routes";
+import { ServerMode, isValidServerMode } from "./config/serverModes";
 import { logger } from "./tux";
 
 export interface RemixMdxConfig {
@@ -628,6 +628,8 @@ export async function resolveConfig(
     }
   }
 
+  logFutureFlagWarnings(future);
+
   return {
     appDirectory,
     cacheDirectory,
@@ -692,3 +694,53 @@ export function findConfig(
 
   return undefined;
 }
+
+function logFutureFlagWarning(args: { flag: string; message: string }) {
+  logger.warn(args.message, {
+    key: args.flag,
+    details: [
+      `You can use the \`${args.flag}\` future flag to opt-in early.`,
+      `-> https://remix.run/docs/en/2.13.1/start/future-flags#${args.flag}`,
+    ],
+  });
+}
+
+export function logFutureFlagWarnings(future: FutureConfig) {
+  if (!future.v3_fetcherPersist) {
+    logFutureFlagWarning({
+      flag: "v3_fetcherPersist",
+      message: "Fetcher persistence behavior is changing in React Router v7",
+    });
+  }
+
+  if (!future.v3_lazyRouteDiscovery) {
+    logFutureFlagWarning({
+      flag: "v3_lazyRouteDiscovery",
+      message:
+        "Route discovery/manifest behavior is changing in React Router v7",
+    });
+  }
+
+  if (!future.v3_relativeSplatPath) {
+    logFutureFlagWarning({
+      flag: "v3_relativeSplatPath",
+      message:
+        "Relative routing behavior for splat routes is changing in React Router v7",
+    });
+  }
+
+  if (!future.v3_singleFetch) {
+    logFutureFlagWarning({
+      flag: "v3_singleFetch",
+      message: "Data fetching is changing to a single fetch in React Router v7",
+    });
+  }
+
+  if (!future.v3_throwAbortReason) {
+    logFutureFlagWarning({
+      flag: "v3_throwAbortReason",
+      message:
+        "The format of errors thrown on aborted requests is changing in React Router v7",
+    });
+  }
+}
diff --git a/packages/remix-server-runtime/responses.ts b/packages/remix-server-runtime/responses.ts
index 57b13d7e680..424b4296aaa 100644
--- a/packages/remix-server-runtime/responses.ts
+++ b/packages/remix-server-runtime/responses.ts
@@ -41,6 +41,11 @@ export type TypedResponse<T = unknown> = Omit<Response, "json"> & {
  * This is a shortcut for creating `application/json` responses. Converts `data`
  * to JSON and sets the `Content-Type` header.
  *
+ * @deprecated This utility is deprecated in favor of opting into Single Fetch
+ * via `future.v3_singleFetch` and returning raw objects.  This method will be
+ * removed in React Router v7.  If you need to return a JSON Response, you can
+ * use `Response.json()`.
+ *
  * @see https://remix.run/utils/json
  */
 export const json: JsonFunction = (data, init = {}) => {
@@ -50,6 +55,10 @@ export const json: JsonFunction = (data, init = {}) => {
 /**
  * This is a shortcut for creating Remix deferred responses
  *
+ * @deprecated This utility is deprecated in favor of opting into Single Fetch
+ * via `future.v3_singleFetch` and returning raw objects.  This method will be
+ * removed in React Router v7.
+ *
  * @see https://remix.run/utils/defer
  */
 export const defer: DeferFunction = (data, init = {}) => {