Freshwater prawn Macrobrachium lanchesteri is commonly present in the rivers in Setiu Wetland and is regarded as a key health indicator of waterbody. The present study was undertaken to survey the health status of M. lanchesteri in Nyatoh and Chalok Rivers in Setiu Wetland. Prawns were sampled from each river by seining for bacterial, mycological and viral screenings, as well as histopathogical examination. Bacterial screening was done using tryptic soy agar (TSA), glutamate starch phenol red (GSP) agar, thiosulfate citrate bile salts sucrose (TCBS) agar, pseudomonas agar F, xylose lysine dextrose (XLD) agar, eosin methylene blue (EMB) agar and horse blood agar. Identifications were done by Gram staining, oxidase and indole tests and BBL Crystal Identification System. Selected isolate was also identified by BLAST® analysis of 16S rRNA gene sequence. Fungi were isolated using potato dextrose agar (PDA) with penicillin G (100 U ml–1) and streptomycin (100 μg ml−1) identified by macro and micromorphologies and BLAST analysis of internal transcribed spacer (ITS) sequence. Viral screening was done for white spot syndrome virus (WSSV), Monodon baculovirus (MBV) and infectious hematopoietic and hypodermal necrosis virus (IHHNV) by polymerase chain reaction. A total of 14 isolates were obtained from the prawn hepatopancreas and eggs including Pseudomonas aeruginosa, Enterobacter spp., Klebsiella spp, Enterococcus spp., Aerococcus viridans and Kluyvera cryocrescens. The P. aeruginosa isolate (N5) was beta hemolytic whereas all other isolates were alpha hemolytic. Mycological screening isolated mostly Ascomycetes sp. Other fungi isolated were Fusarium sp., Galactomyces sp., Basidiomycete sp. and Trichosporon sp. The prawns were tested negative for WSSV, MBV and IHHNV. Histopathology revealed degeneration of hepatopancreas tubule cells and loss of the typical star-shaped lumen in cross-section profile in the samples from the Chalok River. Samples from the Nyatoh River also exhibited tubular degeneration, loss of the star-shaped lumen profile and reduced lumen size. Isolate N5 from Nyatoh River could be potentially pathogenic and of public health concern. Further characterizations on antibiotic susceptibility and virulence are needed to determine its pathogenicity. The Fusarium sp. isolate from Chalok River may be pathogenic to penaeid shrimp, thus further study is needed to identify the isolate to the species level. The absence of WSSV, MBV and IHHNV in the present study does not rule out the possible presence of these viruses in M. lanchesteri in Setiu Wetland. The cause of degenerative changes in hepatopancreas tubules could not be determined. In the present study, Pseudomonas aeruginsa and Fusarium sp. isolate may be potentially pathogenic to penaeid shrimp compared to other species.