A warning message appears on your site saying the site contains malware.

Once Google suspects your site has been infected it will flag your site as unsafe. When your site appears in the search results users will see a message like the one below.

This type of warning is usually triggered by a website having redirects to the unsafe content or spam pages. In some cases, this warning will appear if your website has been hacked and is being used to distribute malware. If you ever see this message on a website that you intend to visit, it's best to stay away! Visiting the site could cause your computer to become infected as well.

A message from google search console (Google Webmaster Tools) notifying you about your website being hacked. (This means google has detected malicious code on your site)

Google "Search Console" used to be called "Google Webmaster Tools". Google Search Console is a must-have tool for all site owners as it gives you an incredible amount of information about how your site is doing in search. This free tool Search Console gives site owners loads of tools to check how their site performs. Not only does it show how your site is doing under the hood, but also how searchers see your site in the search results. You’ll get information on keywords and queries that bring traffic, find out which rich search results your content has earned and discover how your mobile site is doing. I strongly advise you to register your website with Google Search Console to fully benefit from all the insights.

If you run a website you should immediately set up Google Search Console.  

Once you are signed in to Google Search Console, visit the "Security Issues" panel and if you see a warning similar to the one below, you'll know whether or not your site has been infected.

Your hosting company disabled your website

In this case your host may have received reports from site visitors that your site has been hacked, their own automated security tools may have alerted them or they may have received alerts from automated systems outside their own company. In either case, they will usually immediately take your site offline.

Some hosting companies have a policy of immediately formatting a server or hosting account that is infected. They do this to prevent the infection spreading to other customers even after the site is offline. This is why it is important to backup your website often.

Emails like the one below are usually sent out via email to notify you that your website has been compromised. While most hosting companies don't provide services to remove malware from your site, they will suggest services like Sitelock or Sucuri for cleaning services. You can even get with your developer to see if they offer any Website Care Packages or Maintenance Packages.

Your website becomes very slow and shows error messages

This is a tricky one because a slow website could be caused by a number of things, but if hackers are using your site as a way to send spam emails it may slow down the entire server and the other sites hosted on it. Slow load time is often an indication of this type of hacking. Most targeted pages are the checkout, payment, login and signup pages. If your page normally loads in 4 seconds and suddenly it takes 10+ seconds to load, that could be a sign that something is wrong.

If you log in to your CMS and find new admin users or FTP accounts that you haven't created.

If you find new admin users, database users, FTP users it is a strong sign that you are hacked. Privileged accounts are left behind by hackers to continue having access to your website and server. Such accounts are used to backdoor your website and access if whenever they wish to.

If your files have been recently modified.

If you notice core system files being recently modified, compare the files to earlier versions to find what has changed. An attacker could have modifies the files to run malicious code, send spam emails or create back-doors to your website.

If there are files with suspicious looking filenames, server-side scripts (.php, .aspx, .py etc) files in upload directories, it is a strong indication that your website is hacked.

Ads & Pop-ups open when visiting your website

If your website visitors see spam advertisements or popups, your website is likely to be compromised due to malicious code injection. Hackers earn money from ad impressions and what better way to get more impressions than by sneaking their ads onto unsuspecting sites. 

Your website is being re-directed to hacked sites

In some cases these sneaky hackers will re-direct your site to a completely different site, and often, an x-rated site. If this is the case they may have placed a redirect code in your files. 

You see a traffic spike, sometimes on pages that don't even exist on your website.

Hopefully you're using some type of analytics to track and monitor your site's visitors because if you are, you'll be able to notice sudden traffic spikes. Hackers will use your hacked website for ‘spamvertising’ which then causes a traffic spike. Spam emails are sent from your server with links to existing or new pages that are created by the hacker.