What type of fishing gear are you using to collect the samples?

Please have a look at this useful researchgate link and PDF attachments.

https://www.researchgate.net/publication/253246367_A_Comparison_of_Methods_for_Sampling_Fish_Diversity_in_Shallow_Offshore_Waters_of_Large_Rivers

Article A Comparison of Methods for Sampling Fish Diversity in Shall...

Kindly see..

http://web2.uwindsor.ca/courses/biology/corkum/PDFs/Lapointe,Corkum%20-%202006(2).pdf

Please see here..

https://www.fs.fed.us/rm/pubs_other/rmrs_2010_pope_k001.pdf

Check here too..

http://www.sciencedirect.com/science/article/pii/S1679007314000140

See here also..

http://wgbis.ces.iisc.ernet.in/energy/lake2009/workshop/FISH%20SAMPLING%20METHODS.pdf

Also to be explored..

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153066

May be seen..

http://www.fao.org/docrep/003/X6841E/X6841E04.HTM

Should be explored..

https://vtechworks.lib.vt.edu/bitstream/handle/10919/46630/Project_Report.pdf?sequence=1

More info here..

http://www.tandfonline.com/doi/pdf/10.1080/02705060.2012.658213

This too may be looked into..

http://www.ozcoasts.gov.au/geom_geol/case_studies/pdf/DWatson_Milestone.pdf

Also check this...

https://en.wikipedia.org/wiki/Stock_assessment

depends on the species under selection

Yes depend on fishes if according to the fish gear mesh size. Also you can use 1 net and do the replicate.

https://www.fs.fed.us/rm/pubs_other/rmrs_2010_pope_k001.pdf

Kindly check..

http://web2.uwindsor.ca/courses/biology/corkum/PDFs/Lapointe,Corkum%20-%202006(2).pdf

Kindly check..

https://www.fs.fed.us/rm/pubs_other/rmrs_2010_pope_k001.pdf

More info..

http://www.richardcondit.org/manuscripts/monitoring_methods/Methods_for_sampling_fishes_in_Panama_streams_7-27-13.pdf

Do you plan to take 5 replicate samples per sampling event per site ? These may not be independant, as with every sampling, fish would be caught and subsequent catches would have less fish to catch from, as well as scaring fish away from the area. It would be better to sample in different areas, at least 25-50 meters apart for the same sampling event on a day.

Hi. Thank you for the replies. By the way, I'm going to use estuarine set bag net (ESBN) to catch the fishes. 

I think it will be fine if you use the same type of gear to obtain 5 representative samples (5 sets of the net) at each site.  However, since you are interested in measuring fish diversity, you should consider how well the gear is going to catch different species.  If the mesh of the net is large, say >5 or 6 cm, then small fish may pass through the mesh without being captured, so you may miss some of the smaller species in an area, which would bias your diversity estimate at each location.  It may be preferable to use multiple types of sampling gear at each location if possible.