When I read your post two things jump out at me:
- Ecological Count Data
- Repeated Measures
The count data may best be handled using negative binomial or Poisson regression (possibly zero truncated as you may have a lot of zero counts). Second you should be worried about the autocorrelation. The ANOVA design you used won't take this into account. You will want to use some sort of model that handles repeated measures.
So the two key terms you'll want to use in your search are count data and repeated measures.