If you're testing pathogens then segregation is going to be a major consideration - I wouldn't want to take this type of testing on in-house unless I had a very large site so that I could (a) put the lab a long way from production, and (b) have enough production/throughput to justify the cost of building and running it.
I really do think you'd need to be analysing quite large numbers of samples to justify creating a lab for this. We have some extremely large customers who don't bother doing these types of tests internally at most sites - they are either sent to external labs, or they have central group labs set up in separate buildings, with full ISO17025 accreditation in place.
Aside from the equipment you'll need someone sufficiently qualified to be able to use it, suitable methods, method validation etc.
I wouldn't expect this to be a cost saving unless the sample volumes are quite significant, and for a bit of environmental monitoring that doesn't sound too likely?