diff --git a/src/common/config.ts b/src/common/config.ts
index 414e9158..4bc02efe 100644
--- a/src/common/config.ts
+++ b/src/common/config.ts
@@ -253,6 +253,13 @@ function parseCliConfig(args: string[]): CliOptions {
         };
 
     const positionalArguments = parsed._ ?? [];
+
+    // we use console.warn here because we still don't have our logging system configured
+    // so we don't have a logger. For stdio, the warning will be received as a string in
+    // the client and IDEs like VSCode do show the message in the log window. For HTTP,
+    // it will be in the stdout of the process.
+    warnAboutDeprecatedCliArgs({ ...parsed, _: positionalArguments }, console.warn);
+
     // if we have a positional argument that matches a connection string
     // store it as the connection specifier and remove it from the argument
     // list, so it doesn't get misunderstood by the mongosh args-parser
@@ -264,6 +271,28 @@ function parseCliConfig(args: string[]): CliOptions {
     return parsed;
 }
 
+export function warnAboutDeprecatedCliArgs(
+    args: CliOptions &
+        UserConfig & {
+            _?: string[];
+        },
+    warn: (msg: string) => void
+): void {
+    let usedDeprecatedArgument = false;
+    // the first position argument should be used
+    // instead of --connectionString, as it's how the mongosh works.
+    if (args.connectionString) {
+        usedDeprecatedArgument = true;
+        warn(
+            "The --connectionString argument is deprecated. Prefer using the first positional argument for the connection string or the MDB_MCP_CONNECTION_STRING environment variable."
+        );
+    }
+
+    if (usedDeprecatedArgument) {
+        warn("Refer to https://www.mongodb.com/docs/mcp-server/get-started/ for setting up the MCP Server.");
+    }
+}
+
 function commaSeparatedToArray<T extends string[]>(str: string | string[] | undefined): T {
     if (str === undefined) {
         return [] as unknown as T;
diff --git a/tests/unit/common/config.test.ts b/tests/unit/common/config.test.ts
index 78257a3c..789febff 100644
--- a/tests/unit/common/config.test.ts
+++ b/tests/unit/common/config.test.ts
@@ -1,6 +1,7 @@
-import { describe, it, expect } from "vitest";
+import { describe, it, expect, vi, beforeEach } from "vitest";
 import type { UserConfig } from "../../../src/common/config.js";
-import { setupUserConfig, defaultUserConfig } from "../../../src/common/config.js";
+import { setupUserConfig, defaultUserConfig, warnAboutDeprecatedCliArgs } from "../../../src/common/config.js";
+import type { CliOptions } from "@mongosh/arg-parser";
 
 describe("config", () => {
     describe("env var parsing", () => {
@@ -605,3 +606,39 @@ describe("config", () => {
         });
     });
 });
+
+describe("Deprecated CLI arguments", () => {
+    const referDocMessage =
+        "Refer to https://www.mongodb.com/docs/mcp-server/get-started/ for setting up the MCP Server.";
+
+    type TestCase = { readonly cliArg: keyof (CliOptions & UserConfig); readonly warning: string };
+    const testCases = [
+        {
+            cliArg: "connectionString",
+            warning:
+                "The --connectionString argument is deprecated. Prefer using the first positional argument for the connection string or the MDB_MCP_CONNECTION_STRING environment variable.",
+        },
+    ] as TestCase[];
+
+    for (const { cliArg, warning } of testCases) {
+        describe(`deprecation behaviour of ${cliArg}`, () => {
+            let cliArgs: CliOptions & UserConfig & { _?: string[] };
+            let warn: (msg: string) => void;
+
+            beforeEach(() => {
+                cliArgs = { [cliArg]: "RandomString" } as unknown as CliOptions & UserConfig & { _?: string[] };
+                warn = vi.fn();
+
+                warnAboutDeprecatedCliArgs(cliArgs, warn);
+            });
+
+            it(`warns the usage of ${cliArg} as it is deprecated`, () => {
+                expect(warn).toHaveBeenCalledWith(warning);
+            });
+
+            it(`shows the reference message when ${cliArg} was passed`, () => {
+                expect(warn).toHaveBeenCalledWith(referDocMessage);
+            });
+        });
+    }
+});