Addition of organic materials for aggregate formation improves different carbon pools in soil system. The carbonaceous compounds act as binding agents but they differ in their impact on stability of aggregates. The aggregate stability varies with the composition of organic manures and their transformations during decomposition into different carbon forms. It is hypothesized that an equivalent dose of organic manures will enhance aggregate stability differently considering that organic sources vary in the contents of humic and non-humic substances. This study was aimed to (i) determine humic and non-humic substances content and conversion rate in the local organic matter sources (ii) develop relation between the organic source and stable aggregate size, and (iii) water flow, organic carbon content and wheat yield differences due to organic amendments applied on equivalent basis. The characterization of local organic matter sources (Farmyard manure, Muncipal solid waste compost and Poultry litter) on the basis of humic and non-humic substances was carried out by incubating the manures at 30 ± 5 ˚C, and sampled at every 30 days interval for six months duration. The manure samples were analyzed for total organic carbon, microbial biomass carbon, total polysaccharides, humic acid and fulvic acid contents. The results showed that organic sources significantly differed in the contents of humic and non-humic substances. Poultry litter had higher concentrations of active carbon pools such as microbial biomass carbon (27.7 g kg-1) and polysaccharides (6.93 mg kg-1) while MSW compost had highest content of humic acid (15.2 g kg-1) than other manures. After characterization, the effect of equivalent levels of the organic manures i.e. control, 0.25 %, 0.5 % and 1 % soil organic carbon on soil physical properties and xx wheat yield was studied by executing a field experiment conducted at two different sites viz., Experimental Farm at AAUR and University Research Farm at Koont for two years (2012 and 2013), using wheat (Cv. Chakwal 50) as a test crop. Total organic carbon, saturated hydraulic conductivity, dry aggregate size distribution, wet aggregate stability of soil, grain yield and total biomass yield of wheat crop were recorded. The total organic carbon status of soil varied non significantly among the amendments. The application of 0.25 % level of FYM and PL at AAUR site significantly increased the mean weight diameter (MWD) of dry aggregates up to 25 % each, as compared to control. At Koont site, the application of FYM (1.0 % level) showed improvement in MWD up to 6.25 % from control. Considering the MWD of wet aggregates, the results showed that the application of 0.25 % level of MSW compost at AAUR site and FYM at the rate of 0.5 % level at Koont site shown significant improvement with the values of 96.5 % and 73.6 %, respectively. The aggregate formation and stability of various aggregate size fractions improved with different sources of carbon. The carbon associated with different sized aggregates was averagely 12.9 g kg-1 with the application of MSW compost. MSW compost stabilized the soil aggregates significantly due to its highest humic acid content, which resulted into increased hydraulic conductivity rate (51 mm h-1) over control (47 mm h-1) in the soil. These results conclude that soil structural stability is dependent on the composition of the applied organic sources particularly their humic acid content.