To add up on the answer provided by Ita, the nature of water during wet season can contribute to the variation in pH. For instance if the rainfall is acidic. The nature of flood water entering the system is dependent on the nature of soil and the vegetation cover. Dilution due to increased amount of water in wet season and concentration due to evaporation in drier season can also contribute the variation.

See:

J Contam Hydrol. 2014 Jun; 161:10–23. doi: 10.1016/j.jconhyd.2014.03.003. Epub 2014 Mar 31.

Acidification of floodplains due to river level decline during drought.

And:

Flood variation and soil nutrient content in floodplain vegetation communities in the Okavango Delta, Okavango Research Institute, which showed 'pH was significantly lower and higher after a high flood in Zones 1 and 6, respectively, than during low flood'.

Soil chemistry of the flood plain and characteristics of the incoming flood water determine the pH variations in the different seasons. You may wish to think in this direction.

The pH of freshwater varies seasonally due to air and water temperature fluctuations which when rises decreases it and when falls increases it. So, there is negative correlation between the temperature and pH. However, there may be several other parameters like dissolved oxygen, electrical conductivity, total alkalinity, and total hardness that affect the pH.

Seasons have substantial effects on the pH status of wetlands. For instance, during the wet season there is bound to be influxes of allochthonous substances that can either increase or decrease the pH of the water body as a function of rainfall or precipitation. Also during the wet season, there's​ bound to be a dilution effect which can make the pH of the water different from what was obtained during the dry season.For example, if the pH of the water was acidic during the dry season but later became alkaline in the wet season this can be explained this:

The alkaline nature of the water during the wet season may be attributed to the influx of bicarbonate substances into the water as a result of surface runoff after precipitation or as a result of dilution effect.

To add up on the answer provided by Ita, the nature of water during wet season can contribute to the variation in pH. For instance if the rainfall is acidic. The nature of flood water entering the system is dependent on the nature of soil and the vegetation cover. Dilution due to increased amount of water in wet season and concentration due to evaporation in drier season can also contribute the variation.

Thank you everyone for your useful information.

The answer provided by Lemma outlines the importance of seasonal variation, as this greatly influences the pH changes.