Have the water tested by a professional who will be able to test and distinquish the levels of Free Available Chlorine and Total (often called Combined) Chlorine. The golden rule is that these two results ideally require to be close to each other, for example, if you have a free level of 2.3ppm and a total or combined level of 2.8ppm then you are in good shape, however, if you have that free of 2.3ppm and a combined of 3.4 then your pool is loaded with Chloramines which are a nitrogen compound and will cause eye irritation. The most common Chloramines are NHCI and NCI these Chlormaines are present from rain, perspiration and urine among other things. The way to reduce the deficit between the two readings is to superchlorinate or shock the pool, this will burn off the Chloramines and bring the combined levels down to equal the free levels which in turn will mean that your pool is full of free available chlorine ready to act as a sanitizer. Check the pH level as this can also be effected by heavy rain as it causes an inbalance in the Alkalinity which in turn allows the pH to "bounce".