I run a fishkeeping website based on a WordPress (PHP) CMS.

I've recently put a fairly complex "filter" into place which searches my content for mentions of fish species profiles and turns them into an active link.

For example,

asdasd this is a test about abdomen to see if the caudal fin will work asdadasdas try again with abdomen and A. panduro and Apistogramma panduro

...becomes

asdasd this is a test about abdomen to see if the caudal fin will work asdadasdas try again with abdomen and <a href="/?p=1703" class="link_species">A. panduro</a> and <a href="/?p=1703" class="link_species">Apistogramma panduro</a>

On the rest of my website, the species are linked with pretty URLs such as /species/apistogramma-panduro/ but due to the way this filter works, the only information I can get access to is the idof the post. As such, I'm using /?p=1703 or whatever the ID is.

What I'd like to know is: how much will this affect my SEO rating/ranking? Will it be detrimental if I don't rewrite the function?

Thanks in advance,