Saltwater intrusion has become a severe issue for the Mekong Delta in Vietnam, especially near the coastline. This issue has led to farmers diversifying from exclusively growing rice to adopting a mixed rice-shrimp system with rice only cultivated in the wet season. However, the nutrient (nitrogen, phosphorus and carbon) cycling and nutrient use efficiency of this system remain poorly understood. To address this knowledge gap, we examined nutrient budgets across 12 farms using integrated rice-shrimp ponds, and in some cases semi-intensive or intensive shrimp grow-out ponds (Penaeus monodon or Penaeus vannamei), over a two-year period (2014–2015). In terms of nutrient budgets, the main nutrient input (92% of the N input, 57% P and 95% C) in the integrated rice-shrimp ponds (IRSPs) came from intake water (excluding C from primary production), while water discharge accounted for the highest output (75% of N output, 41% P, 57% C, excluding C from respiration). The study showed that IRSPs had low dissolved oxygen and high nutrient concentrations which may affect shrimp production. Conversely, salinity levels in the wet season were too high for rice plants thereby affecting rice production. Shrimp survival in the IRSPs was low over the two years (6.3 ± 2.2%), which resulted in the low proportion of nutrients exported from the ponds as harvested shrimp (6% N, 5% P and 10% C). In contrast, the shrimp grow-out ponds (SGOPs), had much higher survival (77.1% for P. vannamei and 59.2% for P. monodon) in three of the six farms where the shrimp survived through to harvest. In these ponds, formulated feed was the highest nutrient input (P. vannamei: 82% N, 75% P and 85% C; P. monodon: 75% N, 55% P and 77% C) with approximately a third of the nutrients being in the shrimp harvest. In our study, nutrients in the IRSPs were used less efficiently than in SGOPs, hence mechanisms to improve shrimp survival and production in IRSPs are urgently needed.