Successful in-sea aquaculture of sponges for metabolite production requires a sound understanding of the effects of environmental factors on explant growth, survival and metabolite biosynthesis. Using short-term experiments, we examined the effects of season, water flow and depth on the culture response of the New Zealand Demospongiae Latrunculia wellingtonensis (Alvarez, Bergquist and Battershill) and Polymastia croceus (Kelly–Borges and Bergquist). Sponge pieces were cultured seasonally for 2 months at depths of 5 and 10 m at three sites close to parent populations but characterised by differing water flow: high, medium and low. Survival of L. wellingtonensis and P. croceus was lowest in summer, possibly because of the relatively higher water temperature increasing stress during translocation. Growth of farmed sponges varied greatly among seasons, being greatest for L. wellingtonensis in winter and P. croceus in spring, and lowest for both species in autumn. Seasonal variation in growth may result from seasonal variation in food abundance and/or periodic investment of metabolic resources in reproduction. Within each season, growth of both species was greatest overall at the high-flow site, with increases up to 12.5% in weight per month. Culture depth influenced the final size of transplanted sponges by interacting with season and water flow. Bioactivity, a measure of metabolite biosynthesis, was high for both species regardless of the environmental condition.