Chemical forms, reactivities and transformation of iron fractions in marshy waters were investigated with cross-flow filtration technique to study the iron environmental behavior. Iron fractions were divided into four parts: acid-labile iron (pre-acidification of unfiltered marshy water samples, > 0.7 μm), high-molecular-weight iron (0.7-0.05 μm), medium-molecular-weight iron (0.05-0.01μm), and low-molecular-weight iron (< 0.01 μm). The cross-flow filtration suggested that iron primarily exist in both the > 0.7 μm and < 0.01 μm size fractions in marshy waters. Rainfall is the key for rain-fed wetland to determine fate of iron by changing the aquatic biochemical conditions. By monitoring the variation of iron concentrations and fractions over three years, it was found that dissolved iron and acid-labile iron concentrations exhibit a large variation extent under different annual rainfalls from 2006 to 2008. The seasonal variation for iron species proved that the surface temperature could control some conversion reactions of iron in marshy waters. Low-molecular-weight iron would convert to acid-labile iron gradually with temperature decreasing. The photochemical reactions of iron fractions, especially low-molecular-weight iron had occurred under solar irradiation. The relative proportion of low-molecular-weight in total dissolved iron ranging from 28.3% to 43.2% were found during the day time, which proved that the observed decreasing concentration of acid lability iron was caused by its degradation to low molecular weight iron.