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In order to study the long term (24 yrs) effect of application of FYM every three years and fertilizer to each season of crops on soil physical properties like bulk density, particle density, expansion, hydraulic conductivity, infiltration rate, soil aggregate and moisture retention capacity and chemical properties like EC, pH and organic carbon of clayey soil under intensive cropping system (Groundnut-Wheat-Sorghum fodder). A replicated field experiment was conducted to start in 1979 in medium black calcareous clayey soil (Vertic Ustochrepts) of the Instructional farm, College of Agriculture, Junagadh Agricultural University, Junagadh Campus, Junagadh. The treatment consist of soil application of FYM @ 25 t ha-1 at every three year in three treatments (T2, T3 and T4) and half NP (T5), half NP + K (T6) and full NP (T7), full NP + K (T8) treatments from chemical fertilizer and control (T1) (no FYM and fertilizer). For this study, soil samples were collected in 2003 at 0-15 cm (D1) and 15-30 cm (D2) in each plot after harvesting of sorghum fodder crop. The result of present investigation revealed that application of FYM @ 25 t ha-1 significantly reduced bulk density of soil. Due to addition of FYM @ 25 t ha-1 and fertilizer increased significantly expansion, porosity and organic carbon content in soil. It also significantly improved per cent soil aggregate (>1 mm). While, the per cent soil aggregate (0.5-1 mm) significantly decreased with application of FYM. The infiltration rate and hydraulic conductivity significantly increased with application of FYM and fertilizer. The moisture retained at 0, 0.01, 0.03, 0.05, 0.1, 0.3, 0.5, 1.0 and 1.5 MPa significantly increased with application of FYM and fertilizer. In all the case, with the increase in tension, there was decrease in the moisture held. The application of FYM and fertilizer significantly increased salt content in soil. But, the values of soil reaction decreased significantly. The values of porosity, expansion, per cent aggregate (0.5-1mm), hydraulic conductivity, pH and EC were significantly higher in surface soil (0-15 cm) as compared to subsurface soil (15-30 cm). The significant interaction effect of depth and treatment (D x T) was observed in case of bulk density, particle density, porosity, expansion, soil aggregation, hydraulic conductivity, soil reaction and organic carbon content in soil. The interaction effect of D x T on moisture retention capacity was also significant at 0, 0.01, 0.03, 0.05, and 0.5 MPa. The combined effect of K x NP was found significant on soil reaction, porosity and particle density in soil. The maximum positive effect on these parameters were recorded with half recommended dose of NP without K application treatment combination. The correlation study showed that the bulk density, porosity and infiltration rate with yield of wheat and sorghum crop had highly significant positive relationship. While, pod and haulm yield of groundnut with these parameters showed negative and non significant relationship. The correlation between grain and straw yield of wheat and fodder yield of sorghum crop with moisture retained at different suctions (0.03, 0.3, 1.0 and 1.5 MPa) was found to be very highly significant at 1 per cent level. To evaluate the changes in soil characteristics with long term (24 yrs) under intensive cropping system over initial status of soil indicated that moisture retention capacity (14.41 per cent), porosity (14.0 per cent), soil aggregation (13.98 per cent) and infiltration rate (18.36 per cent) increased due to improved organic carbon content (28.30 per cent) in soil under manured and fertilizer treatments. Again balance fertilizer (Full NP + K) produced favourable soil physical and water transmission properties of soils over their initial values.