Abstract An improved esterase method was used to measure the lysis rate of natural phytoplankton in the non-stratified southern part of the North Sea during July and September 2000. Low nutrient concentrations indicated that phytoplankton was controlled by nutrients in July. The average values for silicate, phosphate, ammonium, nitrite, and nitrate were 1.75 ± 1.2, 0.072 ± 0.06, 0.73 ± 0.56, 0.04 ± 0.03, and 0.35 ± 0.44 μM, respectively (n = 24). The average underwater irradiance of the water column was 355 ± 133 Wh m–2 d–1. In autumn (cruise from 11 to 22 September 2000), the phytoplankton grew under light-control. In this period, the average water column irradiance was much lower (i.e. 90 ± 36 Wh m–2 d–1) than during summer because of lower incident irradiance levels and higher turbidity of the water column. Major dissolved inorganic nutrients were higher in September than in July: the average values for silicate, phosphate, ammonium, nitrite, and nitrate were 2.24 ± 1.03, 0.22 ± 0.05, 1.13 ± 0.65, 0.16 ± 0.32, and 0.68 ± 0.85 μM, respectively (n = 24). The average specific lysis rate of plankton was relatively low in September (0.04 ± 0.02 d–1, n = 24), and high in July (i.e. 0.20 ± 0.10 d–1, n = 24). Within each season, the plankton lysis rate correlates with the prevailing average underwater irradiance level at the various stations. The specific lysis rate of plankton was correlated with the total viral abundance (6 × 106–32 × 106 ml–1) in September. The virus density was lowest in turbid waters. In July, viruses were more abundant (20 × 106–48 × 106 ml–1). However, the substantially higher lysis rates in July could not be explained exclusively on the basis of enhanced virus abundance. It is concluded that nutrient-limitation during summer is a stress factor that causes losses to plankton communities by lysis of cells, additional to viral infection.