Field sampling: Research cruises were conducted on& R/V Neeskay and R/V Osprey. Water samples were collected using 5-liter Niskin sampling bottles suspended on a 1/4" cable from a hydrographic winch. Immediately after collection, samples were transferred to 4-liter HDPE sample bottles. Sample bottles were rinsed with sample water 3 times before filling. Prior to use, sample bottles were acid washed (48 hours in 5% HCl), followed by multiple rinses with distilled, deionized water. Samples in bottles were stored in a cooler on ice until return to the laboratory. Samples were filtered immediately upon return to the laboratory (usually less than 8 hours after collection). Samples were filtered through pre-combusted Whatman GF/F filters. Filters were retained for particulate Phosphorus (P), stable isotope (particulate Carbon (C) and Nitrogen (N)), and chlorophyll a analyses. At least twice during the field season, field blanks are collected, which consist of clean bottles brought into the field where they are filled with distilled water, followed by analysis for dissolved and particulate phosphorus.

Nutrients: Samples were collected and analyzed as described in Mosley and Bootsma (2015). Soluble Reactive Phosphorus (SRP) was analyzed using the standard molybdate method and a 10 cm path length in the spectrophotometer. Total Dissolved Phosphorus (TDP) and Particulate Phosphorus (PP) were digested to convert to phosphate, followed by analysis with the standard molybdate method. SRP and TDP were measured within 12 hours of sample filtration.

Chlorophyll a: Samples were collected and analyzed as described in Mosley and Bootsma (2015). Chl a was extracted with a 68:27:5 methanol-acetone-deionized water extraction solvent for 24 hours at -28 degrees Celsius and measured on a Turner Model 10 Series fluorometer, which was calibrated using a chlorophyll extract, the concentration of which was determined spectrophotometrically (Stainton et al. 1977).

CO₂ / DIC: Samples for CO2 and Dissolved Inorganic Carbon (DIC) analyses were collected in stoppered 120 mL glass serum bottles. Prior to sampling, bottles were flushed with nitrogen gas and then evacuated, to ensure they contained no CO2. At the time of sampling, a double-ended needle was inserted into the discharge tube of the Niskin bottle while water was flowing out, and the other end of the needle was inserted through the rubber cap of the serum sample bottle, allowing the vacuum in the bottle to draw in the sample water. The bottle was filled approximately 3/4. CO2 and DIC analyses were carried out following the method described by Davies et al. (2003). Briefly, 50 microliter (uL) subsamples are taken from the bottle headspace using a pressure-lok syringe and injected into a gas chromatograph, calibrated with CO2 standard gases. Samples are run in triplicate. Dissolved CO2 is then determined based on the temperature-dependent solubility of CO2, corrected for CO2 lost to the headspace and for the change in inorganic carbon species distribution accompanying the CO2 loss to headspace. Following CO2 analysis, samples are acidified by adding 150 uL of concentrated phosphoric acid, converting all inorganic carbon to CO2, after which the above analysis was repeated to determine total dissolved inorganic carbon concentration. In-lake CO2 concentrations are determined by correcting for any difference between in situ temperature and temperature at time of analysis, which affects the inorganic carbon partitioning coefficients. CO2 samples were measured within 24 hours of collection, and DIC samples were measured within 3 days of collection.

Continuous CO2: The components of the continuous CO2 monitoring system include a peristaltic pump that forces water through an air-water equilibrator (Membrana mini-module membrane contactor). Reverse-flow air from the equilibrator is pumped through desiccant, after which it flows through an infrared gas analyzer (Li-Cor Li-820) which measures the partial pressure of CO2 normalized to 1 atmosphere. The system also includes a temperature sensor and a WETLabs flow-through fluorometer. The system is controlled by a Campbell CR1000 Controller / Datalogger. Input from a GPS on the ship's upper deck allows all data to be geo-referenced. The system is mounted in the engine room of the Lake Express high-speed ferry, where it draws water from a sea chest that has a residence time of several seconds. Additional details are provided in Zagorski and Bootsma (2006).

Stable isotopes: Samples for stable isotope (13C:12C and 15N:14N ratios) analyses were collected by filtering lake water samples through GF/F glass fiber filters (nominal pore size = 0.7 to 0.8 micrometers (um)). Following filtration, filters were doused with 5% HCl for ~ 3 minutes to remove any inorganic carbon, followed by rinsing with distilled, deionized water. Filters were then freeze dried and packed in tin foil disks. Samples were then analyzed on an isotope ratio mass spectrometer, following the methods as described in Turschak et al. (2014). After every 12th sample, an acetanilide control was run to ensure instrument calibration.

Dissolved organic carbon: 25 ml of filtered water was transferred to an amber glass ampule and acidified to a pH of less than 2 by adding 2-3 drops of 1 N hydrochloric acid (HCl), converting all inorganic carbon to CO2, which was then purged from the sample bubbling with carbon-free gas prior to OC analysis. DOC was then measured using the combustion catalytic oxidation method on a total organic carbon analyzer (Shimadzu TOC-L analyzer equipped with an ASI-5000 auto sampler). The analyzer was calibrated with a dilution series of reagent grade potassium hydrogen phthalate in 0.3 molar hydrochloric acid.