You can add
\makeatletter
\@addtoreset{equation}{section}
\makeatother
to your preamble in order to reset the equation counter with every new section. The above usage doesn't change the representation of the
equation counter. Alternatively, the
chngcntr package provides
\usepackage{chngcntr}
\counterwithin{equation}{section}
which will do the same, but also ensure that the equation counter has a <section>.<equation> format. Similarly, if you're already using amsmath, you can do
\usepackage{amsmath}
\numberwithin{equation}{section}