Seaweed aquaculture biosecurity measures were implemented at the farm level to assess their effectiveness on the occurrence of diseases and epiphytes, correlation of environmental parameters to disease occurrence, and effect on the growth rate and carrageenan properties on the commercially important red seaweeds Kappaphycus alvarezii and Eucheuma denticulatum in Zanzibar, Tanzania. The experiments covered two seasons (cold season; July–September 2020 and hot season; January-March 2021). A significantly lower disease and epiphyte occurrence in K. alvarezii (50% and 38%) and E. denticulatum (45% and 31%) was observed for the bio-secured seaweed farm compared with the non-bio-secured farm during the cold and hot season, respectively. Disease incidence for K. alvarezii and E. denticulatumwas correlated to temperature (p < 0.05) and salinity (p < 0.05). Kappaphycus alvareziiexhibited a significantly higher specific growth rate (SGR) (1.97–3.52%) at the bio-secured farm compared to non-bio-secured farm for both seasons and E. denticulatum had a greater SGR (3.05%) during the hot season. The carrageenan yield and gel strength were significantly higher for healthy seaweed species compared with infected seaweeds (i.e., exhibiting signs of disease and/ or epiphytes) cultured during the cold and hot seasons, respectively. These data clearly show that disease and epiphyte outbreaks can significantly reduce the SGR, carrageenan yield and gel strength in K. alvarezii and E. denticulatum, and that these effects can be influenced by season. Farm level biosecurity practices, however, can effectively reduce disease and epiphyte occurrence and enhance seaweed growth for both K. alvarezii and E. denticulatum.