The influence of habitat, waterfowl abundance, and hunting on winter survival of waterfowl is not well understood. We studied late August–March survival of 163 after-hatch-year (AHY) and 128 hatch-year (HY) female mallards (Anas platyrhynchos) radiotagged in Sacramento Valley (SACV) and 885 AHY female northern pintails (A. acuta) radiotagged throughout the Central Valley of California, USA, relative to flooded habitat (HAB), January abundance of each species (JMAL or JPIN), hunter-days (HDY), and a hunting pressure index (HPI) that combined these variables. From EARLY (1987–1994) to LATE (1998–2000), HAB increased 39%, JPIN increased 45%, JMAL increased 53%, HDY increased 21%, duck-hunting season increased from 59 days to 100 days, and the female daily bag limit doubled to 2 for mallards but remained 1 for pintails. Survival (± SE) was greater during LATE versus EARLY for pintails radiotagged in each region (SACV: 93.2 ± 2.1% vs. 87.6 ± 3.0%; Suisun Marsh: 86.6 ± 3.2% vs. 77.0 ± 3.7%; San Joaquin Valley: 86.6 ± 3.1% vs. 76.9 ± 4.1%) but not for SACV mallards (AHY: 70.6 ± 7.2% to 74.4 ± 7.7% vs. 80.1 ± 7.2% to 82.8 ± 5.6%; HY: 48.7 ± 9.1% [1999–2000 only] vs. 63.5 ± 8.8% to 67.6 ± 8.0%). Most pintail (72%) and mallard (91%) deaths were from hunting, and lower HPI and higher JPIN or JMAL were associated with reduced mortality. Increased HAB was associated with reduced winter mortality for pintails but not for SACV mallards. Pintail survival rates that we measured were within the range reported for other North American wintering areas, and during LATE were higher than most, even though our study duration was 68–110 days longer. Winter survival rates of SACV mallards were also within the reported range. However, with higher bag limits and longer seasons, mallard survival during LATE was lower than in most other wintering areas, especially during 1999–2000, when high winds on opening weekend resulted in high hunting mortality. Habitat conservation and favorable agriculture practices helped create a Central Valley wintering environment where natural mortality of mallards and pintails was low and survival varied with hunting mortality. We recommend regulations and habitat management that continue to minimize natural mortality while allowing sustainable harvest at a level that helps maintain strong incentive for management of Central Valley waterfowl habitats, including the large portion that is privately owned.