Mulwaree Chain of Ponds is a geomorphically rare aquatic system in eastern Australia. Apparently stable and in a highly altered agricultural setting, these ponds are uncharacteristic of local river systems. The deep, large ponds are connected by shallow, vegetated and discontinuous preferential flow paths. Margins of the ponds are vegetated by aquatic, mostly rhizomatous or stoloniferous plants, including Cycnogeton procera, Vallisneria gigantea, Phragmites australis and Eleocharis sphacelata. Once flow is disconnected during summer, these ponds become strongly stratified related to dissolved oxygen, temperature and electrical conductivity; and with a euphotic depth (z1%) of up to 6 metres. This unusual ecosystem provided an opportunity to investigate some of the functional processes driving production, respiration and decomposition during connected and disconnected flow periods. Use of light and dark bottles, combined with phytoplankton methods and C. procera leaf decomposition, has enabled initial understanding of the ecology of this rare system. Light and dark bottles were incubated insitu at depths mid-pond and at three points in the vegetated margins for 24 hours to investigate community production, with chlorophyll A, nutrients and water quality also measured. The results suggested that these chain of ponds act as small monomictic lakes, with seasonal stratification as flows cease. Leaf litter bags with mesh size 9 mm and 150 micron and cotton strips were used to measure total, microbial and standardised decomposition respectively over 21-28 days, mid-pond and within the vegetated margins. Maximum mean gross production at the pond surface (562 mg/m3/d), during mid-summer, significantly declined below the oxycline (30 mg/m3/d) during disconnection. These patterns were not reliably matched by chlorophyll A levels at the same sample points. Total to microbial leaf litter decomposition was strongly seasonal and dominated by microbes. Additionally, small individual pond effects such as cattle grazing and recreational activities altered pond dynamics.