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The weather plays a big part in the wildlife at Paxton Pits. Cold weather can bring more wildfowl, but long periods of frozen conditions may drive birds farther south or lead to some birds starving. Wet weather in spring can flood the nests of birds, but make it easier for wading birds to feed. Dry weather in summer can make the ground hard and dry, reducing the food for many species. Mild weather in winter and early spring can encourage wildlife to start breeding early and wild flowers to start blooming. East Anglia is the driest part of Britain.

The Environment Agency maintains records of rainfall each month, using daily data collected at Great Paxton, on the opposite bank of the river to the nature reserve. Their figures show that after very low levels of rainfall in 1995 and 1996, we have typically had a wet year followed by a dry one until the last three years. 2005 was dry (11 months drier than the 7 year average) and most of 2006 was exceptionally dry until the autumn. Indeed, January and June 2006 were both drier than those months during the previous decade. Of particular note is the variability of rainfall of any month in different years.

The River Great Ouse has burst its banks, entering the reserve, more frequently in recent years. When the river is in flood, the road from St Neots is frequently closed, and the Ouse Valley Way is impassable along the Great Meadow and the Moorings.

2006-2009 monthly rainfall graphs