A monitoring programme was established in order to support community based seaweed farming in south-west Madagascar by providing scientific information on the effects of physico-chemical and health factors influencing the growth of Kappaphycus alvarezii (cottonii). Six aquaculture site configurations were studied. These consisted of high and low flow locations, off-bottom and long-line farming techniques, and different benthic/substrate types. At each site a number of growth and health variables were monitored monthly between January 2012 and March 2013 on 30 randomly selected thalli. Variables included thallus level growth, intensity of epiphyte and disease infection, intensity of fish and sea urchin grazing, and cover of pest seaweed and sediment. The following key environmental variables were also monitored at the site level: water temperature, irradiance, salinity, water depth, wave action, pH and oxygen content. Overall average relative growth rate of K. alvarezii in the region was 4.5 ± 0.06% day-1 and varied by site and season. Generally, growth rate was higher during the winter season (April-August: 5.04 ± 0.31% day-1) than in the summer (3.90 ± 0.28% day-1). The long-line farming technique provided higher growth (5.46 ± 0.09% day-1) than the off-bottom technique (3.99 ± 0.07% day-1). Thallus level analysis showed that fish grazing, epiphyte cover and sediment cover and disease had significant negative correlations with growth, and the four variables were positively correlated. Site level analysis on the effects of physico-chemical and health factors showed that sedimentation, daily maximum of water temperature and variability, and interactions between these factors, were the main determinants of growth. Growth was lower at high sedimentation levels and higher values of maximum temperature and temperature variation. Our findings highlight that farming should focus mainly in the cold season and long-line technique in order to limit the major ecological constraints encountered and maintain growth and production at sustainable levels.