Land-based bivalve aquaculture depends on large-scale cultures of live microalgae for food. The intensity of large-scale microalgal production is important for cost-effectiveness. Using Walne’s medium as the control, simplified media containing nitrogen, phosphorus, silica, iron, manganese and vitamins were designed to determine the impact of nitrogen source and molar N:P ratio (sodium nitrate, NO3 9:1, ammonium chloride, NH4 9:1 and NH4 25:1) on growth, dry-weight biomass, culture longevity and lipid content of Chaetoceros muelleri, a diatom commonly used in shellfish aquaculture. During the exponential phase (day 6), dry-weight production in simplified media was similar to controls, indicating that this microalga can grow successfully on simplified media and use ammonium as the nitrogen source. The cultures grown on nitrate or ammonium differed in their time-course. Low nitrogen concentration in cultures grown with nitrate caused the collapse of these cultures within 11–13 days, after a short stationary phase. Cultures grown with ammonium had a longer stationary phase and were still alive on day 20, in spite of the low nitrogen concentrations observed after day 13 in cultures grown with NH4 9:1. During stationary phase (day 18) there was an increase in lipid content of algae under conditions of low nitrogen availability (NH4 9:1) and extended low phosphorus availability (NH4 25:1). Considering dry weight production, culture longevity, nutrient efficiency and lipid composition, simplified media containing ammonium, phosphorus, silica, iron, manganese and vitamins are a viable and profitable choice for batch culture of C. muelleri. In the exponential phase, the simplified medium NH4 9:1 was as effective as the control. Overall, both of the simplified media using ammonium are effective and suitable, depending on the purpose of the cultures and whether lipid contents (NH4 9:1), dry weight biomass (NH4 25:1) or nitrogen input and output (NH4 9:1) are desired.