Milkfish (Chanos chanos) pond farming in coastal Sidoarjo, Indonesia, shows unequal productivity among smallholder farms operating within the same brackishwater production region. This study quantified farm-level productivity gaps and identified measured technical, economic, environmental and operational variables associated with productivity variation. Field data were collected from 30 active milkfish farmers. Productivity was calculated as harvest output per pond area per production cycle and evaluated against the best-observed productivity benchmark of 4.72 ton ha⁻¹ cycle⁻¹. The analyzed variables were feed conversion ratio, feed cost, operational cost, dissolved oxygen, salinity, ammonia and labor involvement. Average productivity was 3.39 ton ha⁻¹ cycle⁻¹, leaving a mean productivity gap of 1.33 ton ha⁻¹ cycle⁻¹ and an average achievement ratio of 71.92%. Cost per harvested output showed the strongest empirical signal, with a significant negative association with productivity (Spearman correlation coefficient (ρ) = -0.564; p = 0.001). Ammonia and feed conversion ratio showed technically consistent negative directions, although their statistical support was limited. The results indicate that low-productivity farms mainly require better cost-output conversion, improved feed-use efficiency and stronger waste-pressure control rather than simple input expansion.