Fish farmers’ dependence on costly formulated fish feed has affected their income. The cost of formulated feed is also constantly rising. Efforts to mass-produce the locally available natural resource, namely water flea (Moina sp.), were initiated as an alternative to the commercially formulated fish feed. This study evaluates the most suitable growth medium for commercially culturing Moina sp. and Chlorella sp. and studies the effect of their growth activity on water quality. In this study, the growth behaviour of Moina sp. and Chlorella sp. was monitored individually before Moina sp. was cultured together with Chlorella sp. in a growth medium. Chlorella sp. was cultured in different mediums (BG-11, Bristol, and organic fertiliser). The first generation of Moina sp. took 96 h to mature and begin to reproduce, while the next generation took a shorter time (from 24h to 48 h). The brood size was between five and 15 neonates, while the maximum brood count recorded was eight. The Chlorella sp. culture had grown well on Day 5 (555.33 ug/L); thus, it was introduced with Moina sp. on Day 6. Although an organic fertiliser medium provided the optimum conditions for Chlorella sp. growth, it slightly inhibited the Moina sp. growth due to higher ammonia (NH3) concentration. However, the organic fertiliser medium could sustain Chlorella sp. growth while being ingested by Moina sp. The growth activity of both species slightly affected the water quality. Meanwhile, the increase in ammonia (NH3), carbon dioxide (CO2), and calcium carbonate (CaCO3) was recorded. In conclusion, organic fertiliser is the best medium for Chlorella sp. growth, which is the main food source for Moina sp. culture.