The invention discloses an in-situ treatment method of fresh water aquaculture wastewater. The in-situ treatment method comprises the following specific steps: taking dried anaerobic ammonia oxidationgranular sludge as an inner core, taking polyvinyl alcohol, sodium alginate and silicon dioxide as outer-layer embedding agents, embedding bacillus amyloliquefaciens and nitrifying bacteria to prepare composite flora embedded spheres, taking the composite flora embedded spheres as a reaction filler, filling the composite flora embedded spheres into a grid wall to form a water-permeable biologicalreaction wall, and growing periphyton in an attached growth manner, so as to realize in-situ remediation of fresh water aquaculture wastewater. The immobilized microorganism technology can realize synchronous removal of organic matters, ammonia nitrogen and nitrite, and has the characteristics of high microorganism concentration, good activity, strong environmental tolerance and the like; meanwhile, the fresh water aquaculture wastewater is remediated in situ by utilizing the embedded spheres, disturbance to beneficial microorganisms in an ecological system is reduced, the water quality of the water body is stabilized, and the ecological balance of the raw water body is kept.