Effects of excessive fertilizer and manure applications on the soil environment were compared in greenhouse vegetable systems shifted from wheat–maize rotations 5–15 years previously and in wheat–maize rotations. N, P and K surpluses to the greenhouses were 4328, 1337 and 1466 kg ha −1 year −1, respectively compared to 346, 65 and −163 kg ha −1 year −1 to wheat–maize fields. Subsequently, substantial mineral N and available P and K accumulated in the soil and leaching occurred down the soil profile in the greenhouses. Soil pH under vegetables was significantly lower than in the wheat–maize fields, while the EC was significantly higher in the vegetable soils. The mean Cd concentration in the vegetable soils was 2.8 times that in the wheat–maize rotations. Due to excessive fertilizer application in greenhouse vegetable production in northeast China, excessive salt and nitrate concentrations may accumulate and soil quality may deteriorate faster than in conventional wheat–maize rotations. Extremely high nutrient inputs to intensively managed vegetable crops in northeast China may lead to very serious degradation of soil and water quality.