Water samples are collected from fifteen wells in Zubair, Berjesia and Safwan regions/ Basrah Province / Iraq during season 2014. Water samples properties are determined and classified to three categories for salinity (1-4 , 4-8 , and 8-12 dSm-1) and three categories for boron toxicity (< 0.7 , 0.4-3.0, and > 3.0) mg L-1. Water samples water treated with nine mineral and organic filters (Sand filter, charcoal, cement klint dust, porcelain, ash rice husks, barley straw, sawdust, date palm fiber, and poultry manure). Removal efficiency of salinity and boron toxicity is calculated after passing wells water samples throw filters. Results indicated there are differences among filters in decreasing water salinity as following rice hush ash> cement klint dust> barley> straw> poultry manure> sawdust> coal> porcelain> palm fiber> sand for water salinity and boron toxicity of Berjesia , Safwan and Zubair respectively rice husk ash> cement klint dust> coal> porcelain> sawdust> barley> poultry manure> palm fiber> sand and rice husk ash> cement klint dust> coal> porcelain> barley> sawdust = poultry manure> palm fiber> sand for wells in Zubair. After water treatment with filter is used for tomato irrigation planted in field soil of Agricultural Research station / Berjesia. After 176 days of tomato planted, yield was calculated for tomato fruits. Results indicate that there are significant differences among filters in total yield of tomato. Rice husk ash gave highest yield with significant difference. Yield of tomato for rice husk ash, cement klint dust, sand filter and control treatment in Zubair and Berjesia is (989.53, 874.84, 486.02, 375.23) and (870.32, 729.84, 434.07, 176.59) gm pot-1 respectively, and in safwan region was (842.68, 679.86, 358.56, 0.0) gm pot-1 respectively. Filters efficiency in increasing tomato yield was as follows : rice husk ash > cement klint dust > sand filter.