The Karatoa-Atrai River is a trans-boundary river in Bangladesh that was one of the main branches of the old course of the Teesta River before the great earthquake and flood of 1787. After the Teesta had abandoned its old route, Karatoa-Atrai gradually degraded and was entirely cut off from the original Teesta. At present, the Karatoa-Atrai originates in a beel, or depressed area, of Baikunthapur in India and initially enters into Bangladesh (latitude 26°280 and longitude 88°360 ) at Bardeshwari in Panchagarh district. It runs towards the south up to Sahamjhiaghat before entering India again and running for 50 km within India. The river re-enters Bangladesh (latitude 25°100 and longitude 88°460 ) at Naogaon, flows southward, meets the Little Jamuna (this Jamuna is not the Brahmaputra-Jamuna, it is another river flowing through the district of Naoga) near Rasulpur, and ultimately falls at Hurasagar. This is a long river with a total length of about 455 km. For the present analysis, the river has been divided into two reaches, namely, Karatoa and Atrai. The upper reach is considered to be Karatoa, which extends from Panchagarh to Dinajpur before entering into India, and the lower reach is considered to be Atrai, when it re-enters into Bangladesh from Naogaon and flows up to its outfalls at Hurasagar River. According to the data availability of at least 25 years of record, five discharge measurement stations and ten water level measurement stations of Bangladesh Water Development Board (BWDB) were selected for the study. The record length varies considerably. The smallest record length is 25 years and the largest is 50 years. The average record length is 33 years and the standard deviation is 9.1 years. In addition to the measured fortnightly discharge dataset, daily (generated) mean discharge data (up to 2006/07) that are stored at BWDB were also collected.There is no widely accepted single flow value or threshold level that will better characterize low flows concerning the conservation of natural morphology and ecosystem or aquatic organisms. Therefore, threshold level selection of an in-stream flow is critical. The value is dictated by a function of the objectives pursued. Notably, an extensive amount of literature exists on the selection of approaches to determine in-stream (or environmental) flow requirement of rivers (Baghel et al., 2018; Sharma, 2019). These are called in-stream flow methods because they deal with flows ‘in the stream’. There is no single technique or combination of techniques that satisfy all conditions of rivers. In a review of the status for determining environmental flows, Tharme (2003) recognized the existence of 207 individual methodologies, recorded in 44 countries around the world. These methodologies are broadly categorized into four major distinct methods: hydrological, hydraulic rating, habitat simulation and holistic/integrated methodologies (Zeiringer et al., 2018). As far as low-flow studies of Bangladesh are concerned, several important works have estimated the in-stream flow of several rivers, namely, the Surma, Kushiyara (Bari & Marchand, 2006), Teesta (Mullick et al., 2013), Gorai (Moly et al., 2015; Rahman et al., 2017), Dudhkumar (Hossain & Hosasin), Halda (Akter & Ali, 2012), Turag (Rahman et al., 2013), Ganges (Gain et al., 2011), etc. The National Water Management Plan (NWMP) of Bangladesh reported month-wise dependable flows for major and regional rivers assessed by frequency analysis of monthly flow data (WARPO, 2000). The NWMP also considered the minimum flow requirement of the Lower Meghna River, studied by Chowdhury & Haque (1990). Decade-wise changes in discharge were reported for the Gumti River (Chowdhury, 1979), Ganges and Brahmaputra (Chowdhury & Hossain, 2003; Mondal et al., 2010). However, in general, discharge measurements are rarely precise in the low-flow range. The lack of available (quality) data is generally a problem, especially in low-flow analyses. Regionalized methods are often used for transferring information about low-flow, especially to ungauged basins as depicted by Blöschl (2013), Laaha et al. (2013), and Salinas et al. (2013). Furthermore, low-flow frequency analyses and FDC methods were mostly performed through various distribution statistics for different regions of Bangladesh, namely, studies by Bari & Islam (2006) and Bari & Sadek (2002).