How to protect yourself from a flood on a web server?

Question

PHP

How can you protect yourself from a flood on a web server?
The nginx + php-fpm bundle is used, today I encountered such a problem that connections began to multiply, thereby creating php-fpm processes and creating a lot of requests to the mysql server.
I tried limit_conn / limit_req, iptables limits, but as I understand it, the flood came from different addresses, nothing showed in the logs.
Used VDS on DigitalOcean: 2cpu/2gb
Ubuntu 14.04 LTS