During June-October 2005, water quality data were collected from Upper Klamath and Agency Lakes in Oregon, and meteorological data were collected around and within Upper Klamath Lake. Data recorded at two continuous water quality monitors in Agency Lake showed similar temperature patterns throughout the field season, but data recorded at the northern site showed more day-to-day variability for dissolved oxygen concentration and saturation after late June and more day-to-day variability for pH and specific conductance values after mid-July. Data recorded from the northern and southern parts of Agency Lake showed more comparable day-to-day variability in dissolved oxygen concentrations and pH from September through the end of the monitoring period. For Upper Klamath Lake, seasonal (late July through early August) lows of dissolved oxygen concentrations and saturation were coincident with a seasonal low of pH values and seasonal highs of ammonia and orthophosphate concentrations, specific conductance values, and water temperatures. Patterns in these parameters, excluding water temperature, were associated with bloom dynamics of the cyanobacterium (blue-green alga) Aphanizomenon flos-aquae in Upper Klamath Lake. In Upper Klamath Lake, water temperature in excess of 28 degrees Celsius (a high stress threshold for Upper Klamath Lake suckers) was recorded only once at one site during the field season. Large areas of Upper Klamath Lake had periods of dissolved oxygen concentration of less than 4 milligrams per liter and pH value greater than 9.7, but these conditions were not persistent throughout days at most sites. Dissolved oxygen concentrations in Upper Klamath Lake on time scales of days and months appeared to be influenced, in part, by bathymetry and prevailing current flow patterns. Diel patterns of water column stratification were evident, even at the deepest sites. This diel pattern of stratification was attributable to diel wind speed patterns and the shallow nature of most of Upper Klamath Lake. Timing of the daily extreme values of dissolved oxygen concentration, pH, and water temperature was less distinct with increased water column depth. Chlorophyll a concentrations varied spatially and temporally throughout Upper Klamath Lake. Location greatly affected algal concentrations, in turn affecting nutrient and dissolved oxygen concentrations - some of the highest chlorophyll a concentrations were associated with the lowest dissolved oxygen concentrations and the highest un-ionized ammonia concentrations. The occurrence of the low dissolved oxygen and high un-ionized ammonia concentrations coincided with a decline in algae resulting from cell death, as measured by concentrations of chlorophyll a. Dissolved oxygen production rates in experiments were as high as 1.47 milligrams of oxygen per liter per hour, and consumption rates were as much as -0.73 milligrams of oxygen per liter per hour. Dissolved oxygen consumption rates measured in this study were comparable to those measured in a 2002 Upper Klamath Lake study, and a higher rate of dissolved oxygen consumption was recorded in dark bottles positioned higher in the water column. Data, though inconclusive, indicated that a decreasing trend of dissolved oxygen productivity through July could have contributed to the decreasing dissolved oxygen concentrations and percent saturation recorded in Upper Klamath Lake during this time. Phytoplankton self-shading was evident from a general inverse relation between depth of photic zone and chlorophyll a concentrations. This shading caused net dissolved oxygen consumption during daylight hours in lower parts of the water column that would otherwise have been in the photic zone. Meteorological data collected in and around Upper Klamath Lake showed that winds were likely to come from a broad range of westerly directions in the northern one-third of the lake, but tended to come from a narrow range of northwesterly directions